Vallat, B;
Tauriello, G;
Bienert, S;
Haas, J;
Webb, BM;
Žídek, A;
Zheng, W;
... Westbrook, JD; + view all
(2023)
ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.
Journal of Molecular Biology
, Article 168021. 10.1016/j.jmb.2023.168021.
(In press).
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Abstract
ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.
| Type: | Article |
|---|---|
| Title: | ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models |
| Location: | Netherlands |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.jmb.2023.168021 |
| Publisher version: | https://doi.org/10.1016/j.jmb.2023.168021 |
| Language: | English |
| Additional information: | ©2023 The Author(s). Published by Elsevier Ltd.This is an open access article under the CC BY license (http://creativecommons.org/ licenses/by/4.0/). |
| Keywords: | Computed Structure Models, Data Standard, ModelCIF, PDBx/mmCIF, Protein Structure Prediction |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10167512 |
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